RetrogeneDB ID: retro_cfam_1013

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:25044697..25044907(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSCAFG00000002809
• Aliases: None
• Description: high mobility group nucleosomal binding domain 3 [Source:HGNC Symbol;Acc:12312]

Sequence

>retro_cfam_1013
CAGAGAAAGCCTCCAGAGAATACAGAAGACAAGGATAGATCCAAAGCAACTAAATAGGAGACCACCAGACTGTCTGCCAG
ATTGTTAGCAAAACCCACTCCACCAAAACCTGAACCTAAACCAAGAAAAACATCTGCTAACAAAGAACCTGGAACAAAGA
CTAACAAAGGTACCAAAGGAAAGAGGGAGAGCAAGAAGCTGGAAAGCAAG

Alignment

ORF - retro_cfam_1013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 54.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RNKSPENTEGKDGSKVTKQEPTRRSARLSAKPAPPKPEPKPRKTSAKKEPGTKINKGAKGKKEEKQEAGK
          ..K.PENTE.KD.SK.TK.E.TR.SARL.AKP.PPKPEPKPRKTSA.KEPGTK.NKG.KGK.E.K....K
Retrocopy QRKPPENTEDKDRSKATK*ETTRLSARLLAKPTPPKPEPKPRKTSANKEPGTKTNKGTKGKRESKKLESK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.00 RPM	51.15 RPM
SRP017611_brain	0.00 RPM	14.53 RPM
SRP017611_kidney	0.00 RPM	66.57 RPM
SRP017611_liver	0.00 RPM	13.05 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1013 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1013 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011031	1 retrocopy	retro_amel_1920,
Bos taurus	ENSBTAG00000001422	2 retrocopies	retro_btau_1524, retro_btau_1558,
Canis familiaris	ENSCAFG00000002809	1 retrocopy	retro_cfam_1013 ,
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Callithrix jacchus	ENSCJAG00000010800	2 retrocopies	retro_cjac_1626, retro_cjac_819,
Mustela putorius furo	ENSMPUG00000018092	1 retrocopy	retro_mputfur_1164,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Pongo abelii	ENSPPYG00000016791	1 retrocopy	retro_pabe_421,